MD options - Revision history

Uttiyo: /* Electronic stopping */

2024-03-29T10:11:20Z

Electronic stopping

Uttiyo at 13:55, 6 November 2023

2023-11-06T13:55:06Z

Uttiyo at 13:51, 6 November 2023

2023-11-06T13:51:23Z

Uttiyo: /* Non-adiabatic processes */

2023-11-06T13:42:52Z

Non-adiabatic processes

Uttiyo: /* Adaptive time */

2023-11-06T13:39:06Z

Adaptive time

Uttiyo: /* Electronic stopping */

2023-11-06T13:36:01Z

Electronic stopping

Uttiyo at 13:00, 6 November 2023

2023-11-06T13:00:40Z

Uttiyo at 10:09, 26 September 2023

2023-09-26T10:09:52Z

Miguel Caro at 07:27, 30 July 2021

2021-07-30T07:27:23Z

Miguel Caro: Created page with "Molecular dynamics simulations are invoked with the `turbogap md` command. The most important options in the input file that you need to worry about are: #..."

2021-07-30T05:58:55Z

Created page with "Molecular dynamics simulations are invoked with the <code>turbogap md</code> command. The most important options in the input file that you need to worry about are: #..."

New page

[[Molecular dynamics]] simulations are invoked with the <code>turbogap md</code> command. The most important options in the [[input file]] that you need to worry about are:

# <code>[[md_step]]</code>: the time step for [[velocity Verlet]] integration;
# <code>[[md_nsteps]]</code>: the number of time steps to propagate the atomic positions;
# <code>[[thermostat]]</code>: formalism to keep the temperature constant (or not);
## <code>[[t_beg]]</code>: the initial thermostating temperature if a thermostat is chosen;
## <code>[[t_end]]</code>: the final thermostating temperature if a thermostat is chosen;
## <code>[[tau_t]]</code>: the time constant for the thermostat, if chosen;
# <code>[[barostat]]</code>: formalism to keep the pressure constant (or not);
## <code>[[p_beg]]</code>: the initial barostating pressure if a barostat is chosen;
## <code>[[p_end]]</code>: the final barostating pressure if a barostat is chosen;
## <code>[[tau_p]]</code>: the time constant of the barostat, if chosen;
## <code>[[gamma_p]]</code>: the inverse compressibility of the system if a thermostat is chosen;
## <code>[[barostat_sym]]</code>: selects which degrees of freedom of the simulation box are affected by the barostating;
# <code>[[scale_box]]</code>: determines whether the simulation box is scalend during the simulation;
# <code>[[box_scaling_factor]]</code>: determines by how much the box will be increased during the simulation;
# <code>[[write_thermo]]</code>: how often to write out thermodynamic information;
# <code>[[write_xyz]]</code>: how often to write out detailed trajectory information;
# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.

@@ Line 42: / Line 42: @@
 ## <code>[[eel_freq_out]]</code>: how often to write the EEL data to file;
 ## <code>[[estop_filename]]</code>: name of the file containing electronic stopping power data;
 == Non-adiabatic processes ==

@@ Line 19: / Line 19: @@
 # <code>[[write_xyz]]</code>: how often to write out detailed trajectory information;
 # <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
-# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.
+# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds;
-# <code>[[make_group]]</code>: to make a group of atoms in the simulation system
+# <code>[[make_group]]</code>: to make a group of atoms by a definite style in the simulation system.

← Older revision		Revision as of 13:51, 6 November 2023
Line 20:		Line 20:
	# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;		# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
	# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.		# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.
		+	# <code>[[make_group]]</code>: to make a group of atoms in the simulation system

@@ Line 45: / Line 45: @@
 # <code>[[nonadiabatic_processes]]</code>: formalism(s) to account for electronic stopping and electron-phonon coupling;
 ## <code>[[eph_fdm_option]]</code>: choice to activate/deactivate updating of electronic temperature;
 ## <code>[[eph_friction_option]]</code>: choice to activate/deactivate friction forces;

@@ Line 27: / Line 27: @@
 # <code>[[adaptive_time]]</code>: formalism to perform MD with variable time-steps;
 ## <code>[[adapt_tstep_interval]]</code>: interval at which the algorithm is called to calculate a new time-step;
 ## <code>[[adapt_tmin]]</code>: minimum limit of time-step;
 ## <code>[[adapt_tmax]]</code>: maximum limit of time-step;
 ## <code>[[adapt_xmax]]</code>: maximum allowed displacement by an atom per time-step;
 ## <code>[[adapt_emax]]</code>: maximum allowed energy transfer by an atom per time-step;
 == Electronic stopping ==

@@ Line 36: / Line 36: @@
 # <code>[[electronic_stopping]]</code>: formalism(s) to estimate electronic energy loss (EEL) of atoms;
 ## <code>[[eel_cut]]</code>: lower energy cutoff below which no EEL is to be calculated;
 ## <code>[[eel_freq_out]]</code>: how often to write the EEL data to file;

@@ Line 4: / Line 4: @@
 # <code>[[md_nsteps]]</code>: the number of time steps to propagate the atomic positions;
 # <code>[[thermostat]]</code>: formalism to keep the temperature constant (or not);
 ## <code>[[t_beg]]</code>: the initial thermostating temperature if a thermostat is chosen;
 ## <code>[[t_end]]</code>: the final thermostating temperature if a thermostat is chosen;

← Older revision		Revision as of 10:09, 26 September 2023
Line 19:		Line 19:
	# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;		# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
	# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.		# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.
		+
		+
		+	There are also various additional features which can be invoked through different input options. A number of useful features are also currently being developed. These features will suite specific purposes.
		+
		+	== Adaptive time ==
		+
		+	# <code>[[adaptive_time]]</code>: formalism to perform MD with variable time-steps;
		+	## <code>[[adapt_tstep_interval]]</code>: interval at which the algorithm is called to calculate a new time-step;
		+	## <code>[[adapt_tmin]]</code>: minimum limit of time-step;
		+	## <code>[[adapt_tmax]]</code>: maximum limit of time-step;
		+	## <code>[[adapt_xmax]]</code>: maximum allowed displacement by an atom per time-step;
		+	## <code>[[adapt_emax]]</code>: maximum allowed energy transfer by an atom per time-step;
		+
		+	== Electronic stopping ==
		+
		+	# <code>[[electronic_stopping]]</code>: formalism(s) to estimate electronic energy loss (EEL) of atoms;
		+	## <code>[[eel_cut]]</code>: lower energy cutoff below which no EEL is to be calculated;
		+	## <code>[[eel_freq_out]]</code>: how often to write the EEL data to file;
		+	## <code>[[estop_filename]]</code>: name of the file containing electronic stopping power data;
		+
		+	== Non-adiabatic processes ==
		+
		+	# <code>[[nonadiabatic_processes]]</code>: formalism(s) to account for electronic stopping and electron-phonon coupling;
		+	## <code>[[eph_fdm_option]]</code>: choice to activate/deactivate updating of electronic temperature;
		+	## <code>[[eph_friction_option]]</code>: choice to activate/deactivate friction forces;
		+	## <code>[[eph_random_option]]</code>: choice to activate/deactivate random forces;
		+	## <code>[[eph_betafile]]</code>: name of file containing electronic stopping coupling parameter data;
		+	## <code>[[eph_Tinfile]]</code>: name of file containing electronic parameters and mesh for finite difference method (FDM);
		+	## <code>[[eph_box_limits]]</code>: lower and higher boundaries on three directions to construct mesh for FDM;
		+	## <code>[[eph_rho_e]]</code>: scaling parameter for FDM mesh;
		+	## <code>[[eph_C_e]]</code>: electronic heat capacity per unit volume;
		+	## <code>[[eph_kappa_e]]</code>: electronic thermal conductivity;
		+	## <code>[[eph_Ti_e]]</code>: initial electronic temperature;
		+	## <code>[[eph_gsx]]</code>: number of grids in x-direction;
		+	## <code>[[eph_gsy]]</code>: number of grids in y-direction;
		+	## <code>[[eph_gsz]]</code>: number of grids in z-direction;
		+	## <code>[[eph_fdm_steps]]</code>: number of steps for integration of heat diffusion equation;
		+	## <code>[[eph_md_last_step]]</code>: last step of MD in previous run in case of restarted run;
		+	## <code>[[eph_md_prev_time]]</code>: MD time evolved in previous run in case of restarted run;
		+	## <code>[[eph_E_prev_time]]</code>: last value of cumulative electronic energy transfer in previous run in case of restarted run;
		+	## <code>[[eph_freq_Tout]]</code>: how often to write out energy transfer and electronic temperature data;
		+	## <code>[[eph_freq_mesh_Tout]]</code>: how often to write out full map of electronic temperatures;
		+	## <code>[[eph_Toutfile]]</code>: name of the file for electronic temperature map;

@@ Line 13: / Line 13: @@
 ## <code>[[gamma_p]]</code>: the inverse compressibility of the system if a thermostat is chosen;
 ## <code>[[barostat_sym]]</code>: selects which degrees of freedom of the simulation box are affected by the barostating;
-# <code>[[scale_box]]</code>: determines whether the simulation box is scalend during the simulation;
+# <code>[[scale_box]]</code>: determines whether the simulation box is scaled during the simulation;
 # <code>[[box_scaling_factor]]</code>: determines by how much the box will be increased during the simulation;
 # <code>[[write_thermo]]</code>: how often to write out thermodynamic information;

MD options - Revision history

Uttiyo: /* Electronic stopping */

Uttiyo at 13:55, 6 November 2023

Uttiyo at 13:51, 6 November 2023

Uttiyo: /* Non-adiabatic processes */

Uttiyo: /* Adaptive time */

Uttiyo: /* Electronic stopping */

Uttiyo at 13:00, 6 November 2023

Uttiyo at 10:09, 26 September 2023

Miguel Caro at 07:27, 30 July 2021

Miguel Caro: Created page with "Molecular dynamics simulations are invoked with the turbogap md command. The most important options in the input file that you need to worry about are: #..."

Miguel Caro: Created page with "Molecular dynamics simulations are invoked with the `turbogap md` command. The most important options in the input file that you need to worry about are: #..."